MULTIPLE, LARGE DELETIONS IN RAT MITOCHONDRIAL-DNA - EVIDENCE FOR A MAJOR HOT-SPOT

This study identified 33 different deletions in mitochondrial DNA from four aging Fischer-344 rat brains and from a cultured rat lymphoma ce ll line (Nb2 cells). The deletions were located in the longer are betw een the heavy and light strand origins of replication. PCR products th at spanned across the deleted regions were sequenced, and deletions ra nging between 6548 bp and 9977 bp in length were identified. Short dir ect repeats of less than or equal to 8 bp were present at the end poin ts of all but one of the deletions. The remaining deletion contained, instead, a near-perfect direct repeat (9/10 bp) within two base pairs of its end points. In 24 of the deletions, a sequence equivalent to on e member of the paired direct repeats was lost with the deleted segmen t. In the remaining nine, either more or less of the base pairs of a s ingle repeat were lost. Twelve of the 33 different deletions terminate d on one side at a common locus (major hot spot) of 5 bp in length, lo cated at the 5' end of the tRNA(Thr) gene. The opposite ends of these 12 deletions were at different sites. The hot spot was located in a re gion of the mtDNA with strong potential for secondary structure and wa s flanked by a pair of AT-rich sequences. The utilization of the hot s pot as an end point for deletions appeared to be widespread in that it was represented in 1/3-1/2 of the deletions characterized in each of the five mtDNA sources examined. In addition, several minor hot spots, where one end of two or three different deletions coincided, were als o identified.